1. If the crockpot contained only water, even if it had been used for fleishigs within the past 24 hours there is no problem with the hotpot and its water may be used with milchigs. If it contained a fleishig liquid, then the hotpot would need to be kashered.
2. As long as the disposable tablecover is dry and intact, it is sufficient to prevent any transfer of flavor. Of course, if the thin plastic tablecloth tears or melts you will have a problem. If it gets wet you could also potentially have a problem, so I would suggest using a trivet or hot pad under hot food.
3. I would not recommend kashering a microwave (or dishwasher) with soapy water for exactly the reason you mention, it is nearly impossible to remove all the particles of food which is a necessary precondition for kashering.
4. You may begin counting 6 hours from when you conclude eating the meat itself.